Christopher N. Rooper

• Researcher at Fisheries and Oceans Canada

Aim Multivariate spatio‐temporal models are widely applicable, but specifying their structure is complicated and may inhibit wider use. We introduce the R package tinyVAST from two viewpoints: the software user and the statistician. Innovation From the user viewpoint, tinyVAST adapts a widely used formula interface to specify generalised additive...

This study advances the integration of ecosystem information into science advice for fisheries management, focusing on a case study for Pacific Herring (Clupea pallasii ) in Haida Gwaii, British Columbia, Canada. Despite an absence of commercial fishing in recent decades, Haida Gwaii herring productivity has been low, suggesting ongoing impacts fro...

Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data fo...

Sedentary benthic species such as Alcyonacea corals form critical habitat for fishes and invertebrates. Assessing anthropogenic risks to these organisms requires unbiased, species distribution models (SDMs) that attempt to map probabilities of coral presence in relation to bio-physical ocean characteristics; however, in deep-water settings, the acc...

Pacific saury is one of the most economically important species in the northwestern Pacific Ocean. The management of this resource relies on precise input of biological data such as body length and is often hindered by a lack of such data on captured fish. This study explores the potential of electronic monitoring (EM) using off-the-shelf stereo ca...

The Working Group on Small Pelagic Fish (WGSPF) was established to review progress on un-derstanding how environmental and anthropogenic factors influence Small Pelagic Fish (SPF) population dynamics across different ecosystems. The group’s main aim is to foster international and multidisciplinary collaboration to establish comparative analyses and...

Small pelagic fishes occupy an important trophic role in every global aquatic ecosystem, and many species are heavily exploited by fisheries, including some of the largest and most valuable capture fisheries in the world. In November 2022, a symposium on small pelagic fish titled “Small Pelagic Fish: New Frontiers in Science and Sustainable Managem...

Pacific herring Clupea pallasii are a critical commercial and subsistence fish species and play a keystone role in the ecology and culture of the North Pacific. The annual herring spawn, in which mature herring migrate nearshore to deposit eggs along the coastline, is an important event linked to the migration of seabirds and marine mammals as well...

Marine spatial planning and conservation initiatives benefit from an understanding of species distributions across larger geographic areas than are often sampled by any one survey. Here, we test whether the integration of disparate survey data can improve habitat predictions across a region not well sampled by a single survey using Dungeness crab (...

Responses of fish to camera survey gear can influence abundance estimates, and fish behaviors such as attraction or avoidance of an approaching camera platform can bias fish counts. In addition, artificial lighting is generally required for camera-based surveys in boreal systems at > 30 m depth. This study recorded the responses of fish and their a...

Pacific herring Clupea pallasii spawn in nearshore areas in late winter to early spring, but factors influencing the timing and spatial distribution of spawning are not well known. We modeled the temporal and spatial distribution of spawning for 5 herring stocks in British Columbia from egg deposition surveys conducted from 1988-2018 using differen...

Biomass and size composition estimates from the fishery independent biennial Alaska Fisheries Science Center Resource Assessment and Conservation Engineering Division’s Groundfish Assessment Program Gulf of Alaska bottom trawl survey are an integral component of stock assessments and management of fishes in the region. A substantial proportion of t...

Vulnerable marine ecosystems (VMEs), including deep-sea corals and sponges, are important habitats for many fish and invertebrate species and are at risk from the effects of fishing, seafloor mining, and climate change. We describe the zoogeography of deep-sea corals and sponges in Alaska, USA, and identify the environmental factors structuring the...

In the coming decades, warming and deoxygenation of marine waters are anticipated to result in shifts in the distribution and abundance of fishes, with consequences for the diversity and composition of fish communities. Here, we combine fisheries-independent trawl survey data spanning the west coast of the USA and Canada with high-resolution region...

Overview • The Aleutian Islands support high-density coral and sponge communities representing hot-spots of biodiversity • Six "coral garden" sites were protected in 2006, but new surveys and analysis revealed at least 57 new high-density communities in prime fishing depths for several species • Despite extensive protected areas, bycatch of cora...

Pacific halibut (Hippoglossus stenolepis) are a large-bodied species of flatfish that are important culturally, economically, and as a key predator in marine systems in the USA and Canada. The species has a wide distribution, and complex life history including large-scale migrations to spawn and feed, making it potentially susceptible to climate ch...

The North Pacific armorhead (NPA), Pentaceros wheeleri, is thought to exhibit an extended post‐spawning epipelagic phase in which larvae disperse to the northeast Pacific Ocean. Current understanding of juvenile distribution, development, and mechanisms that drive recruitment variation, however, remains largely incomplete. The objective of this stu...

Projecting the future distributions of commercially and ecologically important species has become a critical approach for ecosystem managers to strategically anticipate change, but large uncertainties in projections limit climate adaptation planning. Although distribution projections are primarily used to understand the scope of potential change ‐...

Although species distribution models (SDMs) are commonly used to hindcast fine‐scale population metrics, there remains a paucity of information about how well these models predict future responses to climate. Many conventional SDMs rely on spatially‐explicit but time‐invariant conditions to quantify species distributions and densities. We compared...

Forage fish form a critical trophic link in marine ecosystems, and yet, for many species, there is limited information available. As nations move from single species stock assessments to ecosystem approaches to fisheries management (EAFMs), more information on forage fish will be required. In this study, 50 years of scientific literature were syste...

Pacific sand lance (Ammodytes personatus) support marine food webs in the Salish Sea, yet our knowledge of intertidal spawning habitat for this species is limited. Increasing participation in community science surveys for intertidal sand lance spawning has resulted in the detection of eggs on more than 90 beaches in the Canadian Salish Sea since 20...

Projections of how climate change will impact marine species and communities are urgently needed to inform management measures aimed at stemming biodiversity loss. In the coming decades, warming and deoxygenation of marine waters are anticipated to result in shifts in the distribution and abundance of fishes, with consequences for the diversity and...

To protect cold-water corals and sponges from fishing damage, management changes were made in 2012 to the groundfish bottom trawl fishery British Columbia, Canada. The Groundfish Trawl Habitat Agreement restricted the spatial footprint of the fishery and introduced a cold-water coral and sponge bycatch quota, which was among the world’s first. Usin...

Over the past two decades, numerous ecosystem surveys and process studies have emerged to monitor and assess the large marine ecosystems of Alaska. Several regional collaborative integrated ecosystem research projects (IERPs) were conducted to gain understanding of fish population fluctuations in relation to the surrounding environment. The Gulf of...

Species responses to climate change are often measured at broad spatiotemporal scales, which can miss the fine‐scale changes that are most relevant to conservation and fisheries management. We develop a scaleable geostatistical approach to assess how juvenile and adult fish distributions have been shaped by changes in bottom temperature and dissolv...

Abstract This field guide consolidates the current resources for deep-sea coral taxonomic identification. The field guide covers corals distributed in the eastern North Pacific Ocean including species and taxonomic groups from Alaska, British Columbia and international waters managed by the North Pacific Fisheries Commission. The guide is meant to...

• The Pacific sand lance (Ammodytes personatus) is a key forage species for many commercially important fish (e.g. salmon and groundfish), marine birds, and whales found in nearshore coastal waters of British Columbia, Canada. • Sand lance lack a swim bladder and have a requirement for low-silt, medium-coarse sandy sea-bed habitat for burying. Litt...

Several new species of oviparous skates of the genus Bathyraja have been identified over the past 2 decades, yet it is possible that a complete understanding of species diversity among this group has not been achieved. We used genetics and morphology to screen for the presence of species-level differentiation among embryos from nursery areas in the...

Skate egg case nursery sites are specific locations on the ocean floor where some species of skates deposit egg cases to incubate for up to 5 yr until hatching. We examined genetic diversity within and among skate egg nursery sites of the Alaska skate Bathyraja parmifera and the Aleutian skate B. aleutica in the eastern Bering Sea to gain a better...

Fishery-independent surveys, such as bottom trawl surveys, provide time-series abundance estimates, which inform many modern stock assessments. Area-swept biomass estimates from trawl surveys assume that fish densities do not differ between trawlable (T) and untrawlable (UT) areas. Bias and imprecision in the biomass estimates can occur when this a...

Species responses to climate change are often measured at broad spatiotemporal scales, which can miss fine-scale changes that are relevant to conservation and fisheries management. We develop a scale-able geostatistical approach to assess how juvenile and adult fish distributions have been shaped by changes in bottom temperature and dissolved oxyge...

This review presents updated DFO data on Northern Abalone (Haliotis kamtschatkana) for use in a Committee on the Status of Endangered Wildlife in Canada (COSEWIC) status report. Northern Abalone were frst designated as “Threatened” in 1999 by COSEWIC and re-designated as “Endangered” in 2009, and have been legally listed as “Endangered” under the S...

The National Oceanic and Atmospheric Administration (NOAA) Deep Sea Coral Research and Technology Program (DSCRTP) will conduct a four-year Alaska Coral and Sponge Initiative (2020-2023), which will focus on research in the Gulf of Alaska, Aleutian Islands, and eastern Bering Sea regions. This Science Plan outlines a general strategy for the execut...

Climate-related distribution shifts for marine species are, in general, amplified in northern latitudes. The objective of this study was to predict future distributions of commercially important species in the eastern Bering Sea under six climate scenarios, by incorporating predictions of future oceanographic conditions. We used species distributio...

The National Oceanic and Atmospheric Administration’s (NOAA) Deep Sea Coral Research and Technology Program convened a 4-day virtual science priorities workshop on May 12-15, 2020. The purpose of the workshop was to build partnerships and inform research priorities for the Program’s 4-year Alaska Deep-Sea Coral and Sponge Initiative (2020-2023). A...

Deep-water larval fish and zooplankton utilize structurally complex, cold-water coral and sponge (CWCS) habitats as refuges, nurseries and feeding grounds. Fine-scale sampling of these habitats for larval fish and zooplankton has proven difficult. This study implemented a newly designed, autonomous, noninvasive plankton pump sampler that collected...

The subject matter of this workshop was protection of vulnerable marine ecosystems (VME) in the North Pacific Fisheries Commission (NPFC) Area, with the aim of applying global experiences to the regional assessments and to build capacity to protect VMEs and related management issues in the North Pacific Ocean region. The workshop focused on the mit...

Resource managers in the United States and worldwide are tasked with identifying and mitigating trade-offs between human activities in the deep sea (e.g., fishing, energy development, and mining) and their impacts on habitat-forming invertebrates, including deep-sea corals, and sponges (DSCS). Related management decisions require information about...

Estimating fish condition, the relative weight of an individual fish given its body length, is a convenient way to relate the physiological health and energetic status of fishes to their productivity. Despite evidence of density-dependence effects on condition in some species, previous research has not jointly estimated synchronous changes in condi...

Bottom-contact fisheries present risks to vulnerable marine ecosystems (VMEs) such as deep-water coral and sponge communities. Managing these risks requires better knowledge about VME spatial distribution within fishing areas. In this paper, we develop predictive species distribution models for alcyonacean (Order Alcyonacea) corals at SGaan Kinghla...

Research is needed to determine the seasonal importance of high-relief habitats, particularly those containing biotic structures to rockfishes within the Gulf of Alaska. We examined the density and community structure of commercially important rockfishes in low-relief, high-relief, and biotic habitats in the spring, summer, and winter seasons at th...

The increasing use of underwater cameras to estimate fish abundance often does not account for the behavior of target species. These behaviors can affect detectability of fish and bias density estimates. This study estimated abundance and behavior of several rockfishes (Sebastes spp.) and lingcod (Ophiodon elongatus) at Footprint Bank, a small offs...

Bottom trawl surveys provide fishery‐independent data on relative abundance and life history parameters for a wide range of marine taxa. Survey data are used to assess species distribution, biological interactions, and ecosystem structure and to manage marine resources. Not all bottom types or oceanographic conditions accommodate this survey method...

Cold-water coral and sponge (CWCS) communities are important indicators of vulnerable marine ecosystems (VMEs) and are used to delineate areas for marine conservation and fisheries management. Although the northeast Pacific region of Canada (NEPC) is notable for having unique CWCS assemblages and is the location of >80% of Canadian seamounts, the e...

The role of deep-sea coral and sponge ecosystems as habitat for marine fishes has been widely studied, with many finding significant associations, especially for rockfishes. However, rockfishes also thrive in areas largely devoid of corals and sponges. We compared the use of deep-sea corals and sponges by fish species in two ecosystems. Rockfishes...

In the last two decades the use of species distribution modeling (SDM) for the study and management of marine species has increased dramatically. The availability of predictor variables on a global scale and the ease of use of SDM techniques have resulted in a proliferation of research on the topic of species distribution in the deep sea. Translati...

From late 2014 through 2017, fishery observers in the North Pacific Observer Program, National Marine Fisheries Service, were trained in the identification and sampling of skate egg cases to investigate the interactions between fisheries and skate nursery areas in the eastern Bering Sea. Trained observers identified and assessed 2887 egg cases in a...

Cameras are an important tool for sampling marine environments, providing estimates of fish size and abundance for ecological studies and resource management. In addition to length estimates, calibrated stereo-cameras can be used to provide precise locations (i.e. range and angle) of objects within the view frame of both cameras. We present a gener...

Summary of the cold-water coral and sponge (CWCS) species distribution modelling (SDM) efforts to date. Presents (1) niche separation among major biogenic habitat forming CWCS groups and uses SDM model outputs to spatially test for differences in CWCS habitat suitability among seamounts in the northeast Pacific region of Canada (inside and outside...

Small pelagic fish are key planktivores and prey in marine ecosystems, and their population abundances undergo strong temporal and spatial variability. Top-down (predator controlled) and bottom-up (prey-driven) processes during early life history are important for determining forage fish survival and recruitment. We examined biological and environm...

Deep-sea benthic environments can be home to diverse communities of corals and sponges which are important habitat for marine fishes and invertebrates. From 2010 to 2014, underwater camera surveys in the Aleutian Islands were completed with the objective of evaluating potential effects of substrate type, tidal currents, depth, and fishing pressure...

Defining essential habitats for fishes and invertebrates is an important step in managing groundfish species in Alaska waters. Species distribution models have been widely used to describe the potential habitat of species found in marine and terrestrial systems. The models themselves can take a number of forms, from relatively simple frameworks suc...

Spatial management of vulnerable benthic ecosystem components such as deep-sea corals and sponges requires adequate maps of their distribution. These maps are often based on statistical models of survey data. The objective of this project was to validate the predictions of existing presence or absence and abundance models of deep-sea corals and spo...

Alaska skate species utilize localized egg nursery sites along the interface of the continental slope and shelf in the eastern Bering Sea to lay eggs in high densities. These egg nursery sites persist across years and are thought to be related to environmental conditions. The objective of this analysis was to predict the potential habitat of skate...

Update on the status of Alaskamarineecosystems

To understand and manage marine ecosystems, long-term monitoring of fish biomass is needed. A challenge in estimating fish biomass using sampling nets is varying catchability with habitat, weather, or vessel traffic conditions. Underwater stereo cameras have shown promise in providing a non-lethal, efficient, and cost-effective method to observe an...

Describing essential habitat is an important step toward understanding and conserving harvested species in ecosystem-based fishery management. Using data from fishery-independent ichthyoplankton, groundfish surveys, and commercial fisheries observer data, we utilized species distribution modeling techniques to predict habitat-based spatial distribu...

Defining the essential habitat of federally managed fishes and invertebrates is an important step in managing groundfishes from Alaska. Species distribution models have been widely used in conservation biology and terrestrial systems to define the potential habitat for organisms of interest. The models themselves can take a number of forms, from re...

Defining essential habitats for fishes is important for managing groundfish in Alaska. Species distribution models have been widely used in conservation biology and terrestrial systems to define the potential habitat for organisms of interest. The models themselves can take a number of forms, from relatively simple frameworks such as generalized li...

Deep-sea coral and sponge ecosystems are widespread throughout most of Alaska's marine waters, and are associated with many different species of fishes and invertebrates. These ecosystems are vulnerable to the effects of commercial fishing activities and climate change. We compared four commonly used species distribution models (general linear mode...

When making science matter for conservation, marine conservation practitioners, and managers must be prepared to make the appropriate decision based on the results of the best available science used to inform it. For nearly a decade, many stakeholders encouraged the North Pacific Fishery Management Council to enact protections for deep-sea corals i...

Deep-sea coral and sponge ecosystems are widespread throughout most of Alaska’s marine waters. In some places, such as the central and western Aleutian Islands, deep-sea coral and sponge resources can be extremely diverse and may rank among the most abundant deep-sea coral and sponge communities in the world. Many different species of fishes and in...

Species distribution modeling is a useful tool for informing ecosystems management. However, validation of model predictions through independent surveys is rarely attempted in marine environments, which are challenging to study and often contain sensitive habitats. We conducted an underwater camera survey of the eastern Bering Sea slope and outer s...

Euphausiids (principally Thysanoessa spp.) are found in high abundance in both the eastern Bering Sea (EBS) and the Gulf of Alaska (GOA). They are an important part of these cold-water coastal and pelagic ecosystems as a key prey item for many species, including marine mammals, seabirds, and fish, forming an ecological link between primary producti...

In the Aleutian Islands, patterns of distribution and abundance of Pacific ocean perch (Se-bastes alutus) are influenced by oceanographic processes and bio-genic structures. We used generalized additive modeling (GAM) to examine relationships between these predictors and patterns of settled juvenile and adult distribution and abundance from bottom...

Groundfish that associate with rugged seafloor types are difficult to assess with bottom-trawl sampling gear. Simrad ME70 multibeam echosounder (MBES) data and video imagery were collected to characterize trawlable and untrawlable areas, and to ultimately improve efforts to determine habitat-specific groundfish biomass. The data were collected duri...

This paper describes the design and deployment of a new type of underwater stereo camera capable of triggering when animals are present in the field of view. Unobtrusive evaluation of the camera view field for potential targets is achieved using far-red illumination invisible to most fishes. The triggered camera (TrigCam) system is designed to be l...

Ecosystem management requires information to determine and mitigate adverse impacts of fishing on all ecosystem components. Deep-sea coral and sponge ecosystems often co-occur with fishing activities, and there is considerable research documenting the vulnerability and slow recovery of deep-sea coral and sponge communities to damage. The objective...

Rockfishes (Sebastes spp.) tend to aggregate near rocky, cobble, or generally rugged areas that are difficult to survey with bottom trawls, and evidence indicates that assemblages of rockfish species may differ between areas accessible to trawling and those areas that are not. Consequently, it is important to determine grounds that are trawlable or...

Nursery areas for juvenile fishes are often important for determining recruitment in marine populations by providing habitats that can maximize growth and thereby minimize mortality. Pacific ocean perch (POP, Sebastes alutus) have an extended juvenile period where they inhabit rocky nursery habitats. We examined POP nursery areas to link growth pot...

Rockfishes (Sebastes spp.) are an important component of North Pacific marine ecosystems and commercial fisheries. Because the rocky, high-relief substrate that rockfishes often inhabit is inaccessible to standard survey trawls, population abundance assessments for many rockfish species are difficult. As part of a large study to classify substrate...

Cannibalism is thought to be an inf luential top-down process affecting walleye pollock (Theragra chalcogramma) recruitment in the eastern Bering Sea (EBS). In summer, many age-1 pollock occupy the same depths as those of adult walleye pollock, making them vulnerable to cannibalism. We examine factors that inf luence the occurrence and amount of ca...

Rockfish species are notoriously difficult to sample with multispecies bottom trawl survey methods. Typically, biomass estimates have high coeff icients of variation and can fluctuate outside the bounds of biological reality from year to year. This variation may be due in part to their patchy distribution related to very specific habitat preference...

The abundance of some marine fish species are correlated to the abundance of habitat-forming benthic organisms such as sponges and corals. A concern for fisheries management agencies is the recovery of these benthic invertebrates from removal or mortality from bottom trawling and other commercial fisheries activities. Using a logistic model, observ...

Rockfish are difficult to assess using standard trawl surveys due to their aggregation in high-relief habitats. Therefore, alternative methods are needed to assess rockfish biomass in these habitats. We conducted two experimental acoustic surveys for rockfish in untrawlable habitats in Alaska. One survey was conducted at the Snakehead bank in the G...

English sole (/Pleuronectes vetulus/) is one of a few commercially important marine fishes on the Pacific coast of North America that utilize estuarine areas as nurseries for juvenile stages. English sole recruitment has been linked to environmental conditions occurring during their 6-10 week pelagic egg and larval stages, prior to their appearance...

English sole (Pleuronectes vetulus) is one of a few commercially important marine fishes on the Pacific coast of North America that utilize estuarine areas as nurseries for juvenile stages. English sole recruitment has been linked to environmental conditions occurring during their 6-10 week pelagic egg and larval stages, prior to their appearance i...

Rockfish (Sebastes spp.) biomass is difficult to assess with standard bottom trawl or acoustic surveys because of their propensity to aggregate near the seafloor in highrelief areas that are inaccessible to sampling by trawling. We compared the ability of a remotely operated vehicle (ROV), a modified bottom trawl, and a stereo drop camera system (S...

Many species of rockfishes (Sebastes spp.) are difficult to assess using trawl surveys due to their propensity to aggregate near the seafloor in rocky high relief areas. A feasibility study was conducted during October 2009 in such an area south of Kodiak Island, AK, to evaluate the use of standard fisheries acoustic survey methods in conjunction w...

For those marine fish species with specific habitat preferences, a habitat-based assessment may provide an alternative to traditional surveys. We conducted a habitat-based acoustic and stereo image stock assessment survey for rockfishes (Sebastes spp.) on a rocky ridge habitat in the eastern Bering Sea. Video analysis suggested that juvenile and ad...